Permissions.yml is empty despite the lack of a permissions plugin. Where can I access permissions?

Craftbukkit version: git-Bukkit-e60fc34
Windows 10 Home 64-bit
Java version: "1.8.0_251"
Plugins: dynmap, LagMeter, SetSpawn, Ping, EasyWarps, TreeFellerPlus

Very few people come onto my experimental server I have, so permissions and such are not something that I've looked at a lot. However, commands that I intend for non-opped players to use are for some reason unusable by these players. I did some research and apparently all of the permissions are in permissions.yml, where I should be able to group permissions off of who should be able to use it. However, the file is empty. There are no plugin permissions within the file. I have looked around and I can't find out how to get the permissions onto the file. From what I've read, its usually because there's a permissions plugin that is in use, yet I do not have a permissions plugin. My main question is how do I get all of my permissions back onto permissions.yml? If I can't, then what plugin should I use to take care of this for me without being overly complicated. I don't want to use a plugin that offers way more features than I need while also being overly complicated because I just want to use this server as more of an experimental server with no more than a couple people online at once. I'm also inexperienced with server running and programming, so there may be things that I'll need to be introduced to. Will provide more info if needed. Thanks!

Edit: LuckyPerms seems to have solved the issue I was having with setting up the right command.